Second-half substitutes Masoud Shojaei and Kike Sola did the damage, scoring in the 87th and 90th minutes respectively as Osasuna picked up a fourth win in six matches to climb up to 14th spot, five points above the drop zone.
While the Pamplona side looks to be finding form at just the right time though, Levante is heading in the opposite direction as the loss left it in 10th having now earned just four points from a possible 21.
Levante came into the match on a high after progressing through to the last 16 of the Europa League last week in its maiden European campaign and they would have been desperate to build on that with a win.
And things looked promising enough for the host as it started well with Obafemi Martins only being denied a sixth-minute opener by a brilliant save from Andres Fernandez.
The Osasuna custodian also performed heroics to keep out Martins again 10 minutes later before his Levante counterpart Keylor Navas took centre stage with a brilliant fingertip save to turn over Miguel De las Cuevas' 20-yard drive.
Both sides continued to push for an opener before the break, and Levante was unfortunate not to net in the 39th minute when Sergio Ballesteros hit the post from close range.
That was a let off for Osasuna, but Levante also rode its luck in the 58th minute when the visitor hit the woodwork themselves with a shot from Alejandro Arribas that struck the crossbar.
Navas then produced another fine stop to parry a Emiliano Armenteros shot as Osasuna pushed for a winner.
It was beginning to look like the game would end in stalemate, but Masoud had other ideas.
The Iran international had only been on the pitch six minutes when he broke the deadlock with a brilliant curling effort into the top corner.
Another replacement, Kike Sola, then wrapped up the points with Osasuna's second four minutes into stoppage time as he fired home Armenteros' pass.